Genomic Analyses Revealed the Genetic Difference and Potential Selection Genes of Growth Traits in Two Duroc Lines

Genome-wide selection reveals candidate genes associated with multiple teats in Hu sheep

Increasing the number of teats in sheep helps to improve the survival rate of sheep lambs after birth. In order to analyze the candidate genes related to the formation of multiple teats in Hu sheep, the present study was conducted to investigate the genetic pattern of multiple teats in Hu sheep. In this study, based on genome-wide data from 157 Hu sheep, Fst, xp-EHH, Pi and iHS signaling were performed, and the top 5% signal regions of each analyzed result were annotated based on the Oar_v4.0 for sheep. The results show that a total of 142 SNP loci were selected. We found that PTPRG, TMEM117 and LRP1B genes were closely associated with polypodium formation in Hu sheep, in addition, among the candidate genes related to polypodium we found genes such as TMEM117, SLC25A21 and NCKAP5 related to milk traits. The present study screened out candidate genes for the formation of multiple teats at the genomic level in Hu sheep.

Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

BACKGROUND

Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.

RESULTS

Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.

CONCLUSIONS

In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Genome-wide association study to reveal new candidate genes using single-step approaches for productive traits of Yorkshire pig in Korea

OBJECTIVE

The objective is to identify genomic regions and candidate genes associated with age to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) in Yorkshire pig.

METHODS

This study used a total of 104,380 records and 11,854 single nucleotide polymorphism (SNP) data obtained from Illumina porcine 60K chip. The estimated genomic breeding values (GEBVs) and SNP effects were estimated by single-step genomic best linear unbiased prediction (ssGBLUP).

RESULTS

The heritabilities of AGE, ADG, BF, and EMA were 0.50, 0.49, 0.49, and 0.23, respectively. We identified significant SNP markers surpassing the Bonferroni correction threshold (1.68×10-6), with a total of 9 markers associated with both AGE and ADG, and 4 markers associated with BF and EMA. Genome-wide association study (GWAS) analyses revealed notable chromosomal regions linked to AGE and ADG on Sus scrofa chromosome (SSC) 1, 6, 8, and 16; BF on SSC 2, 5, and 8; and EMA on SSC 1. Additionally, we observed strong linkage disequilibrium on SSC 1. Finally, we performed enrichment analyses using gene ontology and Kyoto encyclopedia of genes and genomes (KEGG), which revealed significant enrichments in eight biological processes, one cellular component, one molecular function, and one KEGG pathway.

CONCLUSION

The identified SNP markers for productive traits are expected to provide valuable information for genetic improvement as an understanding of their expression.

Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs

This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated with LMA, LMD and BFT, respectively, and searched genes within the 1 Mb region near the significant SNPs with relevant functions as candidate genes. Consequently, we identified one (DOCK5), three (PID1, PITX2, ELOVL6) and three (CCR1, PARP14, CASR) promising candidate genes for LMA, LMD and BFT, respectively. Moreover, the multi-trait GWAS identified four significant SNPs associated with the three traits. In conclusion, the GWAS analysis of LMA, LMD and BFT in a DLY pig population identified several associated SNPs and candidate genes, further deepening our understanding of the genetic basis of these traits, and they may be useful for marker-assisted selection to improve the three traits in DLY pigs.

Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations

South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer's extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the identified regions included quantitative loci (QTLs) associated with economically important traits. For example, meat and carcass QTLs were prevalent in all the populations, showing the potential of village and indigenous populations' ability to be managed and improved for such traits. Results of this study therefore increase our understanding of the intricate interplay between selection pressures, genomic adaptations, and desirable traits within South African pig populations.

Heritability estimates and genome-wide association study of methane emission traits in Nellore cattle

The objectives of the present study were to estimate the heritability for daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to perform genome-wide association studies (GWAS) to identify genomic regions and candidate genes influencing the genetic variation of CH4 and CH4res. Methane emission phenotypes of 743 Nellore animals belonging to 3 breeding programs were evaluated. CH4 was measured using the sulfur hexafluoride (SF6) tracer technique (which involves an SF6 permeation tube introduced into the rumen, and an appropriate apparatus on each animal), and CH4res was obtained as the difference between observed CH4 and CH4 adjusted for dry matter intake. A total of 6,252 genotyped individuals were used for genomic analyses. Data were analyzed with a univariate animal model by the single-step GBLUP method using the average information restricted maximum likelihood (AIREML) algorithm. The effects of single nucleotide polymorphisms (SNPs) were obtained using a single-step GWAS approach. Candidate genes were identified based on genomic windows associated with quantitative trait loci (QTLs) related to the 2 traits. Annotation of QTLs and identification of candidate genes were based on the initial and final coordinates of each genomic window considering the bovine genome ARS-UCD1.2 assembly. Heritability estimates were of moderate to high magnitude, being 0.42 ± 0.09 for CH4 and 0.21 ± 0.09 for CH4res, indicating that these traits will respond rapidly to genetic selection. GWAS revealed 11 and 15 SNPs that were significantly associated (P < 10-6) with genetic variation of CH4 and CH4res, respectively. QTLs associated with feed efficiency, residual feed intake, body weight, and height overlapped with significant markers for the traits evaluated. Ten candidate genes were present in the regions of significant SNPs; 3 were associated with CH4 and 7 with CH4res. The identified genes are related to different functions such as modulation of the rumen microbiota, fatty acid production, and lipid metabolism. CH4 and CH4res presented sufficient genetic variation and may respond rapidly to selection. Therefore, these traits can be included in animal breeding programs aimed at reducing enteric methane emissions across generations.

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig

As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber-type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio-temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next-generation sequencing technology, the integration of quantitative trait loci mapping with genome-wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in-depth understanding and utilization remain, and the cost of large-scale sequencing, which requires integrated analyses of high-throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs.

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

BACKGROUND

Pork quality can directly affect customer purchase tendency and meat quality traits have become valuable in modern pork production. However, genetic improvement has been slow due to high phenotyping costs. In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs.

RESULTS

We produced WGS data (18,695,907 SNPs and 2,106,902 INDELs exceed quality control) from 1,469 sequenced Duroc × (Landrace × Yorkshire) pigs and developed a reference panel for meat quality including meat color score, marbling score, L* (lightness), a* (redness), and b* (yellowness) of genomic prediction. The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population. Using different marker density panels derived from WGS data, accuracy differed substantially among meat quality traits, varied from 0.08 to 0.47. Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39% to 75%. We optimized the marker density and found medium- and high-density marker panels are beneficial for the estimation of heritability for meat quality. Moreover, we conducted genotype imputation from 50K chip to WGS level in the same population and found average concordance rate to exceed 95% and r² = 0.81.

CONCLUSIONS

Overall, estimation of heritability for meat quality traits can benefit from the use of WGS data. This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

Effect of early vs. late maturing sire lines and creep feeding on the cortisol response, intestinal permeability, and growth performance of nursery and finishing pigs

A total of 21 litters (11 early and 10 late maturing Duroc × DNA 241) resulting in 241 pigs were used in 170 d trial to determine the effect of sire lines selected for either early or late maturing growth rates and creep feeding on the cortisol concentration, intestinal permeability, and growth performance of nursery and finishing pigs. Treatments were arranged in a 2 × 2 factorial with main effect of Duroc sire line (early or late maturing) and creep feeding (with or without). Creep feed was provided for 14 d prior to weaning. After weaning (approximately 21 d of age; initially 6.4 kg), no interactions were observed for blood cortisol. However, blood cortisol levels were increased (P = 0.011) in late maturing pigs compared to early maturing pigs. A lower percentage (P < 0.001) of early maturing pigs lost weight 3 d post-weaning compared to late maturing pigs. Likewise, early maturing pigs had improved (P < 0.001) average daily gain (ADG) and average daily feed intake (ADFI) during the first 3 d in the nursery and also had increased ADFI (P < 0.001) from days 2 to 14 in the nursery. Creep feeding had no effect on initial nursery performance. On day 7, after a 2-h fast, a subsample of pigs was administered an oral gavage of lactulose and mannitol dissolved in distilled water. No differences by sire line, creep feeding, or their interactions were observed in lactulose:mannitol ratio. For overall nursery growth performance, an interaction was observed for ADG (P = 0.007) and ADFI (P < 0.001), with creep feed providing a benefit in late maturing pigs, but not in early maturing pigs. Early maturing pigs had poorer gain-to-feed ratio (G:F) (P < 0.001) than late maturing pigs. For overall finishing performance, an interaction was observed for ADG (P = 0.037) and ADFI (P = 0.007), with creep feed providing a benefit in late maturing pigs, but not in early maturing pigs. This resulted in an interaction for final body weight (P = 0.005), with late maturing pigs that did not receive creep feed having decreased market weights (P ≤ 0.003) compared to the other treatments. In summary, early maturing pigs had decreased cortisol concentration at weaning and improved ADG and ADFI until approximately 100 kg, at which point late maturing pigs began to exhibit greater ADG. Late maturing pigs had improved G:F from 46 d of age until market. Interestingly, creep feeding late maturing pigs resulted in increased day 170 weight compared with providing no creep feed, whereas creep feed did not impact early maturing pigs (sire line × creep feed interaction, P < 0.005).

Sex effects on carcass characteristics, meat quality traits and meat amino acid and fatty acid compositions in a novel Duroc line pig

In-depth studies of carcass characters and meat quality could provide insight both for breeding improvement and food development in pigs. Breed and gender are two main factors affected the carcass and meat altitude, which plays important roles in pork industry. The aim of this study was to evaluate the sex effects on carcass characteristics and meat quality traits in a novel Duroc strain pig crossbred from French line, American line and Canadian line pigs. A total of 30 pigs (15 surgical-castrated males and 15 females) with similar birthweight (1.8 ± 0.13 kg) was used in experiment. During the experiment period, all pigs were fed same commercial diets. Overall, female pigs observed higher (p < 0.05) carcass weight, slaughter backfat, loin muscle area, loin muscle depth, carcass yield, pH on 45 min, meat histidine and essential amino acid (AA) compositions, and eicosenoic, unsaturation and free fatty acids (FA) compositions compared with meat from castrated males. Whereas, castrated males' meat showed better altitude (p < 0.05) on meat lightness, meat moisture content percentage, total umami AA and stearic acid and saturated FA compositions than those from female ones. In conclusion, the results of this study provide evidence on the sex effects on meat quality and carcass parameters in Duroc strain pigs. Furthermore, this study also give a reference on the relationship between sex and carcass and meat characteristics in Durco strain pigs.

Comparison of meat quality and glycolysis potential of two hybrid pigs in three-way hybrid model

With the improvement of consumers' requirements for pork quality, the method of crossbreeding with excellent local pig breeds to improve meat quality is popular. Saba pig has high reproduction rate, good meat quality and high utilization rate of roughage, but its excellent characteristics have not been fully developed and utilized. To promote the development and utilization of Saba pigs and production of high-quality pork, the meat quality traits and glycolysis potential of Duroc × (Landrace × Yorkshire) (DLY), Berkshire × (Duroc × Saba) (BDS), and Duroc × (Berkshire × Saba) (DBS) three-way crossbred pigs were compared. The results showed that DLY had the highest live weight, carcass weight, lean meat percentage, drip loss, glycolysis potential, muscle diameter, and relative mRNA expression levels of type IIb muscle fibers as well as the lowest ultimate pH (p < 0.05). The lightness value of DBS was the highest (p < 0.05). Among the three crossbred pigs, myristic, arachidic, palmitoleic, and eicosenoic acids were the highest in BDS. These results indicated that the carcass traits of local crossbred pigs were worse than those of DLY pigs, but meat quality was markedly higher, with BDS showing the best meat quality.

Phosphoproteomic analysis identifies differentially expressed phosphorylation sites that affect muscle fiber type in pigs

Skeletal muscle of livestock is composed of both fast- and slow-twitch muscle fibers, which are key factors in their meat quality. However, the role of protein phosphorylation in muscle fiber type is not completely understood. Here, a fast-twitch (biceps femoris, BF) and slow-twitch (soleus, SOL) muscle tissue sample was collected from three male offspring of Duroc and Meishan pigs. We demonstrate that the meat quality of SOL muscle is significantly better than that of BF muscle. We further used phosphoproteomic profiling of BF and SOL muscles to identify differences between these muscle types. A total of 2,327 phosphorylation sites from 770 phosphoproteins were identified. Among these sites, 287 differentially expressed phosphorylation sites (DEPSs) were identified between BF and SOL. GO and KEGG enrichment analysis of proteins containing DEPSs showed that these phosphorylated proteins were enriched in the glycolytic process GO term and the AMPK signaling pathway. A protein-protein interaction (PPI) analysis reveals that these phosphorylated proteins interact with each other to regulate the transformation of muscle fiber type. These analyses reveal that protein phosphorylation modifications are involved in porcine skeletal muscle fiber type transformation. This study provides new insights into the molecular mechanisms by which protein phosphorylation regulates muscle fiber type transformation and meat quality in pigs.

Effects of Dietary Fiber on Growth Performance, Nutrient Digestibility and Intestinal Health in Different Pig Breeds

To explore the effect of dietary fiber on growth performance and intestinal health in different pig breeds, forty Taoyuan and Duroc pigs (pure breeds) of 60 days of age were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 10), and fed with a basal diet (BD) or high-fiber diet (HFD). The trial lasted for 28 d, and results showed that the Taoyuan pigs had a higher average daily feed intake (ADFI) than the Duroc pigs (p < 0.05). The average daily gain (ADG) and digestibilities of gross energy (GE) and crude protein (CP) were higher in Taoyuan pigs than in the Duroc pigs under HFD feeding (p < 0.05). The HFD increased the superoxide dismutase (SOD) and catalase (CAT) activity in Taoyuan pigs (p < 0.05). Interestingly, Taoyuan pigs had a higher jejunal villus height and ratio of villus height to crypt depth (V/C) than the Duroc pigs. The HFD significantly improved the villus height and V/C ratio in duodenum and jejunum (p < 0.05). The HFD also increased the jejunal maltase and ileal sucrase activities in Duroc and Taoyuan pigs, respectively (p < 0.05). Taoyuan pigs had a higher expression level of duodenal fatty acid transport protein-1 (FATP-1) than the Duroc pigs (p < 0.05). Furthermore, the HFD acutely improved the expression levels of ileal SGLT-1 and GLUT-2, and the expression levels of jejunal occludin and claudin-1 in Taoyuan pigs (p < 0.05). Importantly, Taoyuan pigs had a higher colonic Bifidobacterium abundance than the Duroc pigs (p < 0.05). The HFD not only elevated the colonic Lactobacillus abundance and butyrate acid content in Taoyuan pigs, but also increased the acetic and propionic acid contents in both the pig breeds (p < 0.05). These results indicated a difference in dietary fiber (DF) utilization by the two pig breeds, and results may also suggest a beneficial character of DF in regulating intestinal health.

Genome-Wide Association Study and Selective Sweep Analysis Reveal the Genetic Architecture of Body Weights in a Chicken F2 Resource Population

Rapid growth is one of the most important economic traits in broiler breeding programs. Identifying markers and genes for growth traits may not only benefit marker-assisted selection (MAS)/genomic selection (GS) but also provide important information for understanding the genetic architecture of growth traits in broilers. In the present study, an F₂ resource population derived from a cross between the broiler and Baier yellow chicken (a Chinese local breed) was used and body weights from 1 to 12 weeks of age [body weight (BW) 1–BW12)] were measured. A total of 519 F₂ birds were genome re-sequenced, and a combination of genome-wide association study (GWAS) and selective sweep analysis was carried out to characterize the genetic architecture affecting chicken body weight comprehensively. As a result, 1,539 SNPs with significant effects on body weights at different weeks of age were identified using a genome-wide efficient mixed-model association (GEMMA) package. These SNPs were distributed on chromosomes 1 and 4. Besides, windows under selection identified for BW1–BW12 varied from 1,581 to 2,265. A total of 42 genes were also identified with significant effects on BW1–BW12 based on both GWAS and selective sweep analysis. Among these genes, diacylglycerol kinase eta (DGKH), deleted in lymphocytic leukemia (DLEU7), forkhead box O17 (FOXO1), karyopherin subunit alpha 3 (KPNA3), calcium binding protein 39 like (CAB39L), potassium voltage-gated channel interacting protein 4 (KCNIP4), and slit guidance ligand 2 (SLIT2) were considered as important genes for broiler growth based on their basic functions. The results of this study may supply important information for understanding the genetic architecture of growth traits in broilers.

Identification and functional prediction of long non-coding RNAs related to skeletal muscle development in Duroc pigs

Objective

The growth of pigs involves multiple regulatory mechanisms, and modern molecular breeding techniques can be used to understand the skeletal muscle growth and development to promote the selection process of pigs. This study aims to explore candidate lncRNAs and mRNAs related to skeletal muscle growth and development among Duroc pigs with different average daily gain (ADG).

Methods

A total of 8 pigs were selected and divided into two groups: H group (high-ADG) and L group (low-ADG). And followed by whole transcriptome sequencing to identify differentially expressed (DE) lncRNAs and mRNAs.

Results

In RNA-seq, 703 DE mRNAs (263 up-regulated and 440 down-regulated) and 74 DE lncRNAs (45 up-regulated and 29 down-regulated) were identified. In addition, 1,418 Transcription factors (TFs) were found. Compared with mRNAs, lncRNAs had fewer exons, shorter transcript length and open reading frame length. DE mRNAs and DE lncRNAs can form 417 lncRNA-mRNA pairs (antisense, cis and trans). DE mRNAs and target genes of lncRNAs were enriched in cellular processes, biological regulation, and regulation of biological processes. In addition, quantitative trait locus (QTL) analysis was used to detect the functions of DE mRNAs and lncRNAs, the most of DE mRNAs and target genes of lncRNAs were enriched in QTLs related to growth traits and skeletal muscle development. In single-nucleotide polymorphism/insertion-deletion (SNP/INDEL) analysis, 1,081,182 SNP and 131,721 INDEL were found, and transition was more than transversion. Over 60% of percentage were skipped exon events among alternative splicing events.

Conclusion

The results showed that different ADG among Duroc pigs with the same diet maybe due to the DE mRNAs and DE lncRNAs related to skeletal muscle growth and development.

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.